A genome-wide analysis of transcripts in a 2BS.2RL wheat-rye translocation during Hessian fly infestation

Molecular and Cytogenetic Characterization of a Wheat-Rye 7BS.7RL Translocation Line with Resistance to Stripe Rust, Powdery Mildew, and Fusarium Head Blight

Secale cereale is used as a source of genes for disease resistance in wheat cultivation. In this study, a homozygous translocation line (RT14-245) that originated from a cross between a commercial wheat cultivar (Mianyang 11) and a local Chinese variety of rye (Baili) was developed. Multicolor fluorescence in situ hybridization and PCR analysis demonstrated that the translocation chromosome was 7BS.7RL. Resistance analysis showed that RT14-245 was resistant to prevalent pathotypes of stripe rust and powdery mildew. RT14-245 also exhibited high resistance to Fusarium head blight, which was similar to the resistance exhibited by the wheat cultivar Sumai 3. The results indicated that RT14-245 simultaneously exhibited high levels of resistance against stripe rust, powdery mildew, and Fusarium head blight. These results indicate that chromosome arm 7RL in the translocation line RT14-245 is an excellent new resource for wheat breeding programs.

Identification of genome-specific transcripts in wheat-rye translocation lines

Studying gene expression in wheat-rye translocation lines is complicated due to the presence of homeologs in hexaploid wheat and high levels of synteny between wheat and rye genomes (Naranjo and Fernandez-Rueda, 1991 [1]; Devos et al., 1995 [2]; Lee et al., 2010 [3]; Lee et al., 2013 [4]). To overcome limitations of current gene expression studies on wheat-rye translocation lines and identify genome-specific transcripts, we developed a custom Roche NimbleGen Gene Expression microarray that contains probes derived from the sequence of hexaploid wheat, diploid rye and diploid progenitors of hexaploid wheat genome (Lee et al., 2014). Using the array developed, we identified genome-specific transcripts in a wheat-rye translocation line (Lee et al., 2014). Expression data are deposited in the NCBI Gene Expression Omnibus (GEO) under accession number GSE58678. Here we report the details of the methods used in the array workflow and data analysis.

Expression analysis of individual homoeologous wheat genome- and rye genome-specific transcripts in a 2BS.2RL wheat-rye translocation

Wheat-rye translocations are widely used in wheat breeding to confer resistance against abiotic and biotic stress. Studying gene expression in wheat-rye translocations is complicated due to the presence of homoeologous genes in hexaploid wheat and high levels of synteny between wheat and rye chromatin. To distinguish transcripts expressed from each of the three wheat genomes and those from rye chromatin, genomic probes generated from diploid progenitors of wheat and rye were synthesized on a custom array. A total of 407 transcripts showed homoeologous genome ('A', 'B' or 'D' genome)- or rye genome ('R')-specific differential expression, based on unequal values of probe hybridization. In a 2BS.2RL wheat-rye translocation, thirteen of the 407 transcripts showed preferential expressions from rye chromatin. As well as quantifying variation in homoeologous transcript in wheat-rye translocations, this study also provides a potential aid to examine the contribution of the subgenomes to complex allohexapolyploids.